NEW YORK, Dec. 29, 2011 /PRNewswire/ -- Reportlinker.com announces that a new market research report is available in its catalogue:
Molecular Diagnostics - Technologies, Markets and Companies
Benefits of this report
-This report has evolved during the past 15 years, profiting from feedback by numerous readers and experts.
-The most comprehensive and up-to-date one-stop source of information on technical and commercial aspects of molecular diagnostics.
-Includes profiles of 313 companies, the largest number in any report on this topic.
-500 references, cited in the report are included in the bibliography.
-The text is supplemented by 97 tables and 15 figures.
Who should read this report?
-Chief executive officers of molecular diagnostic companies.
-Business development executives of pharmaceutical and biotechnology companies.
-Executives of companies involved in developing integration of diagnosis and treatment as well as those interested in personalized medicine.
-Officers of genomic and proteomic companies interested in diagnostic technologies.
-Research scientists involved in application of molecular diagnostic technologies.
-Planners of healthcare services.
Summary
This report describes and evaluates the molecular diagnostics technologies that will play an important role in practice of medicine, public health, pharmaceutical industry, forensics and biological warfare in the 21st century. This includes several polymerase chain reaction (PCR)-based technologies, fluorescent in situ hybridization (FISH), peptide nucleic acids (PNA), electrochemical detection of DNA, biochips, nanotechnology and proteomic technologies.
Initial applications of molecular diagnostics were mostly for infections but are now increasing in the areas of genetic disorders, preimplantation screening and cancer. Genetic screening tests, despite some restrictions is a promising area for future expansion of in vitro diagnostic market. Molecular diagnostics is being combined with therapeutics and forms an important component of integrated healthcare. Molecular diagnostic technologies are also involved in development of personalized medicine based on pharmacogenetics and pharmacogenomics. Currently, there has been a considerable interest in developing rapid diagnostic methods for for point-of-care and biowarfare agents such as anthrax.
The number of companies involved in molecular diagnostics has increased remarkably during the past few years. More than 500 companies have been identified to be involved in developing molecular diagnostics and 313 of these are profiled in the report along with tabulation of 707 collaborations. Despite the strict regulation, most of the development in molecular diagnostics has taken place in the United States, which has the largest number of companies.
The markets for molecular diagnostics technologies are difficult to estimate. Molecular diagnostics markets overlap with markets for non-molecular diagnostic technologies in the in vitro diagnostic market and are less well defined than those for pharmaceuticals. Molecular diagnostic markets are analyzed for 2011 according to technologies, applications and geographical regions. Forecasts are made up to 2021. A major portion of the molecular diagnostic market can be attributed to advances in genomics and proteomics. Biochip and nanobiotechnology are expected to make a significant contribution to the growth of molecular diagnostics.
This report was first published as DNA Diagnostics in 1995 by PJB Publications, UK. It was updated in 1997 as Molecular Diagnostics and the next edition, Molecular Diagnostics II, was published by Decision Resources Inc in 1999. All the three versions of the reports were well accepted and sold widely.The report has been rewritten several times since then.
Table of Contents
0. Executive Summary 23
1. Introduction 25
Definitions and scope of the subject 25
Historical evolution of molecular diagnostics 25
Molecular biology relevant to molecular diagnostics 26
DNA 26
DNA polymerases 26
Restriction endonucleases 27
DNA methylation 27
RNA 28
RNA polymerases 28
Non-coding RNAs 28
DNA transcription 29
Chromosomes 29
Telomeres 30
Mitochondrial DNA 30
Genes 31
The genetic code 31
Gene expression 31
The human genome 32
Variations in the human genome 32
Variations in DNA sequences 32
Single nucleotide polymorphisms 33
Haplotyping 33
Copy number variations in the human genome 34
Genotype and haplotypes 35
Insertions and deletions in the human genome 35
Complex chromosomal rearrangements 36
Large scale variation in human genome 36
Structural variations in the human genome 37
Replication of the DNA helix 37
Transposons 38
Proteins 38
Proteomics 38
Monoclonal antibodies 39
Aptamers 39
Basics of molecular diagnostics 39
Tracking DNA: the Southern blot 39
Pulsed-field gel electrophoresis 40
DNA Probes 40
The polymerase chain reaction 41
Basic Principles of PCR 41
Target selection 41
Detection of amplified DNA 41
Impact of human genome project on molecular diagnostics 42
Mapping and sequencing of structural variation from human genomes 43
1000 Genomes Project 43
Human Variome Project 44
Role of bioinformatics in molecular diagnostics 45
Systems biology approach to molecular diagnostics 45
Biomarkers 45
Applications of molecular diagnostics 46
2. Molecular Diagnostic Technologies 49
Introduction 49
DNA sample collection and extraction 49
Blood samples 49
Dried blood spots 49
Buccal swabs and saliva 50
Urine samples for transrenal DNA 50
Manual vs automated DNA extraction 51
Sample preparation 51
Pressure Cycling Technology 51
Membrane immobilization of nucleic acids 51
Automation of sample preparation in molecular diagnostics 52
ABI PRISM 6700 Automated Nucleic Acid Workstation 52
BioRobot technology 52
COBAS AmpliPrep System 53
GENESIS FE500 Workcell 53
GeneMole 53
PCR BioCube 53
QIAsymphony 54
Tigris instrument system 54
Techniques for sample preparation that are suitable for automation 54
Xtra Amp Genomic DNA Extraction 54
Extraction of DNA from paraffin sections 54
Dynabead technology 55
Pressure Cycling Technology 55
SamPrep 55
Use of magnetic particles for automation in genome analysis 55
Companies involved in nucleic acid isolation 56
Labeling and detection of nucleic acids 57
Novel PCR methods 57
Addressing limitations of PCR 57
CAST-PCR 58
Combined PCR-ELISA 58
Convection PCR 59
Digital PCR 59
Emulsion PCR 60
ExCyto PCR 60
Long and accurate PCR 60
Multiplex PCR 61
Real-time PCR systems 61
Dyes used in real-time PCR 62
Commercially available real-time PCR systems 62
LightCycler PCR system 63
LightUp probes based on real-time PCR 63
READ™ real-time PCR method 64
StellARray™ technology 64
7500 Fast Dx Real-Time PCR Instrument 64
Applications of real-time PCR 64
Limitations of real-time PCR 65
Quantitative PCR for accurate low level DNA analysis 65
qPCR for quantification of circulating mtDNA 66
Guidelines for real-time qPCR 66
Future applications of real-time qPCR 66
Reverse transcriptase (RT)-PCR 67
Standardized reverse transcriptase PCR 68
Single cell PCR 68
LATE-PCR 68
COLD-PCR 68
AmpliGrid-System 69
DNA melt analysis 70
High-resolution DNA melt analysis for genotyping 70
PCR device for DNA melt analysis in space 70
Monitoring of gene amplification in molecular diagnostics 70
Non-PCR nucleic acid amplification methods 71
DNA probes with conjugated minor groove binder 71
Dynamic Flux Amplification 71
Isothermal reaction for amplification of oligonucleotides 71
ICAN (Isothermal and Chimeric primer-initiated Amplification of Nucleic Acids) 72
Linked Linear Amplification 72
Multiplex Ligation-Dependent Probe Amplification 72
Rapid analysis of gene expression 73
Rolling circle amplification technology 73
Gene-based diagnostics through RCAT 74
RCAT-immunodiagnostics 75
RCAT-pharmacogenomics 75
Circle-to-circle amplification 75
Ramification amplification method 76
Single Primer Isothermal Amplification 76
Transcription mediated amplification 76
WAVE nucleic acid fragment analysis system 77
Technologies for signal amplification 77
3 DNA dendrimer signal amplification 78
Hybridization signal amplification method 78
Signal mediated amplification of RNA technology 79
Invader assays 80
Hybrid Capture technology 81
Branched DNA test 82
Tyramide signal amplification 82
Non-enzymatic signal amplification technologies 82
Direct molecular analysis without amplification 83
Trilogy™ Platform 83
Direct detection of dsDNA 84
Multiplex assays 85
Fluorescent in situ hybridization 85
FISH technique 86
Applications of FISH 86
Modifications of FISH 87
Direct visual in situ hybridization 87
Direct labeled Satellite FISH probes 87
Comparative genomic hybridization 88
Primed in situ labeling 88
Interphase FISH 88
FISH with telomere-specific probes 89
Multicolor FISH 89
Simultaneous Ultrasensitive Subpopulation staining/Hybridization In situ 90
Automation of FISH 90
Companies involved in FISH diagnostics 90
RNA diagnostics 91
RNA isolation from tissue samples 91
Commercially available tests for mRNA detection and quantitation 91
Branched-chain DNA assay for measurement of RNA 92
Cycling probe technology 92
Invader RNA assays 93
Linear RNA amplification 93
Non-isotopic RNase cleavage assay 93
Nucleic acid sequence-based amplification 94
Q Beta replicase system 96
RNAScope 96
RNA expression profiling 96
Visualization of mRNA expression in vivo 96
Solid Phase Transcription Chain Reaction 97
Transcriptome analysis 97
MicroRNA diagnostics 97
Real-time PCR for expression profiling of miRNAs 98
Microarray vs quantitative PCR for measuring miRNAs 98
Use of LNA to explore miRNA 99
Nuclease Protection Assay to measure miRNA expression 99
Microarrays for analysis of miRNA gene expression 99
Modification of in situ hybridization for detection of miRNAs 100
Whole genome amplification 100
Companies that provide technologies for whole genome amplification 101
QIAGEN's Repli-G system 101
GenomePlexÔ Whole Genome Amplification 102
DNA sequencing 102
Companies involved in sequencing 103
Applications of next generation sequencing in molecular diagnostics 105
Companies developing sequencing for molecular diagnostics 105
Genome-wide approach for chromatin mapping 106
Mitochondrial sequencing 106
Identification of unknown DNA sequences 107
Optical mapping 107
Gene expression analysis 108
Gene expression profiling on whole blood samples 108
Gene expression patterns of white blood cells 109
Gene expression profiling based on alternative RNA splicing 109
MAUI (MicroArray User Interface) hybridization 110
Monitoring in vivo gene expression by molecular imaging 110
Serial analysis of gene expression (SAGE) 110
Single-cell gene expression analysis 111
T cell receptor expression analysis 111
Tangerine™ expression profiling 112
Whole genome expression array 112
Ziplex™ system 113
Companies involved in gene expression analysis 113
Peptide nucleic acid technology 114
Use of PNA with fluorescence in situ hybridization 114
PNA and PCR 115
Use of PNA with biosensors 116
PNA-based PD-loop technology 116
PNA-DNA hybrid quadruplexes 117
Companies involved in PNA diagnostics 117
Locked nucleic acids 117
Zip Nucleic Acids 118
Electrochemical detection of DNA 118
Mediated nucleic acid oxidation 119
Detection of hybridized nucleic acid with cyclic voltametry 119
Electrochemical detection based on Toshiba's CMOS technology 120
Concluding remarks on electrochemical DNA detection 120
Bead-based assay platforms 120
Scorpions™ technology 121
The Scorpions reaction 121
Applications of Scorpions 122
Nucleic acid lateral flow molecular diagnostics 122
3. Biochips, Biosensors, and Molecular Labels 125
Introduction to biochip technology 125
Applications of biochips in diagnostics 125
GeneChip 126
GeneChip Human Genome Arrays 127
AmpliChip CYP450 127
Electronic detection of nucleic acids on microarrays 127
Microchip capillary electrophoresis 128
Strand displacement amplification on a biochip 128
Rolling circle amplification on microarrays 128
LiquiChip-RCAT 128
Fast PCR biochip 129
Multiplex microarray-enhanced PCR for DNA analysis 129
Multiplexed Molecular Profiling 129
Universal DNA microarray combining PCR and ligase detection reaction 130
Genomewide association scans 130
Whole genome chips/microarrays 131
Transposon insertion site profiling chip 131
Standardizing the microarrays 132
Companies involved in developing biochip technology for diagnostics 132
Future of biochip technology for molecular diagnostics 133
Microfluidic chips 134
Fish-on-chip 134
Lab-on-a-chip 134
LabCD 135
Micronics' microfluidic technology 135
Microfluidic chips/arrays using PCR 135
Microfluidic automated DNA analysis using PCR 135
Digital PCR Array 135
Digital PCR on a SlipChip 136
Microfluidic chips integrated with RCAT 136
Microfluidic chips integrated with PET 136
Companies developing microfluidic technologies 137
Biosensor technologies 137
Classification of biosensor technologies 138
DNA-based biosensors 139
DNA hybridization biosensor chips 139
PCR-free DNA biosensor 139
DNA based biosensor to detects metallic ions 140
Genetically engineered B lymphocytes 140
Biosensors immunoassays 140
PNA (peptide nucleic acid)-based biosensors 141
Protein-based biosensors 141
Antibody biosensors 141
Cell-based biosensors (cytosensors) 141
Multicell biosensors 142
Microbial biosensors 142
Optical biosensors 143
Surface plasmon resonance technology 143
Label-free optical biosensor 144
Microsensors using with nano/microelectronic communications technology 144
Electrochemical sensors 144
Enzyme electrodes for biosensing 144
Conductometric sensors 145
Electrochemical genosensors 145
Electrochemical nanobiosensor 145
Bioelectronic sensors 146
Phototransistor biochip biosensor 146
Ribozyme-based sensors 146
RiboReporters 147
Concluding remarks and future prospects of biosensor technology 147
Companies developing biosensors for molecular diagnostics 148
Molecular labels and detection 149
Detection technologies for molecular labels 150
Fluorescence and chemiluminescence 150
Fluorescence technologies for label detection 151
Companies with fluorescence and chemiluminescence products 151
Molecular beacons 152
The Green fluorescent protein 153
Multiophoton detection radioimmunoassay 154
Multi-pixel photon counter 154
Enzyme labels and detection by fluorescence 154
Phase-sensitive flow cytometry 155
Microtransponder-based DNA diagnostics 155
Laboratory Multiple Analyte Profile 156
Multiple labels 156
Protein-DNA chimeras for detection of small numbers of molecules 157
Single molecule detection 157
Atomic force microscopy 158
Capillary electrophoresis 158
Confocal laser scanning 158
nCounter Analysis System 158
Spectrally resolved fluorescence lifetime imaging microscopy 159
Molecular imaging 159
Basic research in molecular imaging 160
Devices for molecular imaging 160
Molecular imaging in clinical practice 160
Challenges and future prospects of molecular imaging 161
Companies involved in molecular imaging 161
Nanobiotechnology for molecular diagnostics 161
Magnetic nanoparticles 162
Gold nanoparticles 163
Quantum dot technology 164
Nanotechnology on a chip 165
Nanogen's NanoChip 165
Fullerene photodetectors for chemiluminescence detection on microfluidic chip 165
Diagnostics based on nanopore technology 166
Nanosensors 166
Detection of cocaine molecules by nanoparticle-labeled aptasensors 166
Nanosensors for glucose monitoring 167
PEBBLE nanosensors 167
Quartz nanobalance biosensor 167
Cantilever arrays 167
Resonance Light Scattering technology 168
DNA nanomachines for molecular diagnostics 169
Nanobarcodes technology for molecular diagnostics 169
Qdot nanobarcode for multiplexed gene expression profiling 169
Role of nanobiotechnology in improving molecular diagnostics 170
Companies involved in nanomolecular diagnostics 170
Concluding remarks about nanodiagnostics 173
Future prospects of nanodiagnostics 173
4. Proteomic Technologies for Molecular Diagnostics 175
Introduction 175
Proteomic technologies 175
Biomarkers of disease 175
Proteomic tools for biomarkers 175
Search for biomarkers in body fluids 176
Captamers with proximity extension assay for proteins 176
Cyclical amplification of proteins 176
Detection of misfolded proteins by ELISA with exponential signal amplification 177
Diagnostics based on designed repeat proteins 177
Differential Peptide Display 177
Light-switching excimer probes 178
MALDI-TOF MS 178
Molecular beacon aptamer 179
Molecular beacon assay 179
Proteomic patterns 180
Real-time PCR for protein quantification 180
Protein biochip technologies 181
ProteinChip 182
LabChip for protein analysis 182
TRINECTIN proteome chip 183
Protein chips for antigen-antibody interactions molecular diagnostics 183
Microfluidic devices for proteomics-based diagnostics 183
Nanotechnology-based protein biochips/microarrays 184
Nanoparticle protein chip 184
Protein nanobiochip 184
Protein biochips based on fluorescence planar wave guide technology 184
New developments in protein chips/microarrays 185
Antibody microarrays 185
Aptamer-based protein biochip 186
Multiplexed Protein Profiling on Microarrays 186
Proteomic pattern analysis 186
Single molecule array 187
Viral protein chip 187
Commercial development of protein chips for molecular diagnostics 187
Proteome Identification Kit 189
Laser capture microdissection (LCM) 189
LCM technology 189
Applications of LCM in molecular diagnostics 190
Proteomic diagnosis of CNS disorders 190
Cerebrospinal fluids tests based on proteomics 190
Urine tests for CNS disorders based on proteins in urine 191
Diagnosis of CNS disorders by examination of proteins in the blood 191
Diagnosis of CNS disorders by examination of proteins in tears 192
Role of proteomics in the diagnosis of Alzheimer's disease 192
Role of proteomics in the diagnosis of Creutzfeldt-Jakob disease 193
Future prospects of use of proteomics for diagnosis of CNS disorders 193
Concluding remarks on the use of proteomics in diagnostics 193
5. Molecular Diagnosis of Genetic Disorders 195
Introduction 195
Cytogenetics 196
FISH with probes to the telomeres 196
Single copy FISH probes 196
Comparative genomic hybridization 197
Use of biochips in genetic disorders 197
Representational oligonucleotide microarray analysis 198
SignatureChip®-based diagnostics for cytogenetic abnormalities 198
Diagnosis of genomic rearrangements by multiplex PCR 198
Quantitative fluorescent PCR 198
Mutation detection technologies 199
PCR-based methods for mutation detection 200
Cleavase Fragment Length Polymorphism 200
Direct dideoxy DNA sequencing 200
Digital Genetic Analysis (DGA) 200
Fluorescence-based directed termination PCR 201
Fluorescence melting curve analysis for multiplex mutation detection 201
Heteroduplex analysis 202
Restriction fragment length polymorphism 202
Single-stranded conformation polymorphism (SSCP) analysis 202
TaqMan real-time PCR 203
Non-PCR methods for mutation detection 203
Arrayed primer extension 203
BEAMing (beads, emulsion, amplification, and magnetics) 204
ELISA-protein truncation test 204
Enzymatic mutation detection 204
Specific anchor nucleotide incorporation 205
Conversion analysis for mutation detection 205
Biochip technologies for mutation detection 205
Combination of FISH and gene chips 206
Haplotype Specific Extraction 206
Use of biosensors for detection of mutations 206
Technologies for SNP analysis 207
DNA sequencing 208
Electrochemical DNA probes 208
Use of NanoChip for detection of SNPs 209
Single base extension-tag array 209
Laboratory Multiple Analyte Profile 209
SNP genotyping with gold nanoparticle probes 210
PCR-CTPP (confronting two-pair primers) 210
Peptide nucleic acid probes for SNP detection 210
SNP genotyping on a genome-wide amplified DOP-PCR template 210
Pyrosequencing 211
Reversed enzyme activity DNA interrogation test 211
Smart amplification process version 2 212
Zinc finger proteins 212
UCAN method (Takara Biomedical) 212
Biochip and microarray-based detection of SNPs 213
SNP genotyping by MassARRAY 213
Electronic dot blot assay 213
Biochip combining BeadArray and ZipCode technologies 214
SNP-IT primer-extension technology 214
OmniScan SNP genotyping 214
Affymetrix SNP genotyping array 214
Concluding remarks on SNP genotyping 215
Limitations of SNP in genetic testing 215
Haplotyping versus SNP genotyping 216
Nanofluidics technology for high throughput SNP genotyping 216
Companies involved in developing technologies/products for SNP analysis 216
Role of copy number variations in genetic diagnostic testing 218
CNVs in various diseases 218
CNVs in genetic epilepsy syndromes 218
CNVs associated with schizophrenia 218
Methods for determination of CNVs 219
Digital array for CNV detection 219
Wellcome Trust Case Control Consortium CNV typing array 219
CNVer algorithm for CNV detection 219
Study of rare variants in pinpointing disease-causing genes 220
Prenatal DNA diagnosis 221
Amniocentesis 221
Chorionic villus sampling 221
Separating fetal cells in maternal blood for genetic diagnosis 221
Antenatal screening for Down's syndrome 222
Fetal DNA in maternal blood 222
Molecular methods for prenatal diagnosis 223
aCGH for prenatal diagnosis 223
BAC HD Scan test 223
FISH for prenatal diagnosis 223
PCR for prenatal diagnosis 224
Plasma DNA sequencing to detect fetal chromosomal aneuploidies 224
In vivo gene expression analysis of the living human fetus 225
Noninvasive prenatal diagnosis of monogenic diseases 225
Digital relative mutation dosage 225
Massively parallel plasma DNA sequencing 225
Applications of prenatal diagnosis 226
Diagnosis of congenital infections 227
Diagnosis of congenital CMV 227
Diagnosis of eclampsia 227
Use of transrenal DNA for prenatal testing 227
Preimplantation genetic diagnosis 228
Technologies for preimplantation genetic diagnosis (PGD) 228
PCR for preimplantation genetic diagnosis 228
FISH for preimplantation genetic diagnosis 229
Microarrays for preimplantation genetic diagnosis 229
Conditions detected by preimplantation genetic diagnosis 229
The future of preimplantation genetic diagnosis 230
Companies involved in prenatal/preimplantation diagnosis 231
Cystic fibrosis 232
Detection of CFTR gene mutations 232
CFTR technologies of various companies 232
Genzyme's CF gene sequencing 233
CF PlusÔ Tag-It Cystic Fibrosis Kit 234
Asuragen's bead array test 234
The Ambry CF Test 235
Biochip for CF diagnosis 235
Identification of CF variants by PCR/Oligonucleotide Ligation Assay 235
SensiGene (SEQUENOM) CF carrier screening test 235
Serum proteomic signature for CF using antibody microarrays 236
Guidelines for genetic screening for CF 236
Congenital adrenal hyperplasia 236
Primary immunodeficiencies 237
Hematological disorders 238
Hemoglobinopathies 238
Sickle cell anemia 238
Thalassemia 238
Paroxysmal nocturnal hemoglobinuria 239
Hemophilia 239
Hereditary hemochromatosis 239
Polycystic kidney disease 240
Hereditary metabolic disorders 240
Lesch-Nyhan Syndrome 240
Gaucher's Disease 241
Acute Intermittent Porphyria 241
Phenylketonuria 241
Hereditary periodic fever 242
Achondroplasia 242
Molecular diagnosis of cardiovascular disorders 242
Coronary heart disease 243
Genomics of coronary heart disease 244
Cardiomyopathy 244
Familial Hypertrophic Cardiomyopathy 244
Idiopathic dilated cardiomyopathy 245
Cardiac Arrhythmias 245
Long Q-T Syndrome 245
Familial atrial fibrillation 245
Idiopathic ventricular fibrillation 246
Congestive heart failure 246
Hypertension 246
Disturbances of blood lipids 247
Familial dyslipoproteinemias 247
Hypercholesterolemia 247
Thrombotic disorders 247
Factor V Leiden mutation 248
Pulmonary embolism 248
Hereditary thrombophilia 249
Companies developing molecular diagnostics for cardiovascular disorders 249
Molecular diagnosis of eye diseases 250
Molecular diagnosis of retinitis pigmentosa 250
Genetic screening for glaucoma 250
Role of molecular diagnostics in rheumatoid arthritis 251
Molecular diagnosis of neurogenetic disorders 251
Alzheimer's disease 253
Autism spectrum disorders 253
CNVs associated with autism 253
Charcot-Marie Tooth disease 254
Down syndrome 255
Duchenne and Becker muscular dystrophy 255
eNOS gene polymorphisms as predictor of cerebral aneurysm rupture 256
Fragile X syndrome 256
Huntington disease 257
Hereditary neuropathy with liability to pressure palsies 257
Mitochondrial disorders affecting the nervous system 258
Parkinson's disease 258
Pompe's disease 259
Spinal muscular atrophy 259
Triple repeat disorders 259
Genetic testing for disease predisposition 260
Direct-to-consumer genetic tests 260
6. Molecular Diagnosis of Infections 263
Introduction 263
Molecular techniques for the diagnosis of infections 263
Antibody-enhanced microplate hybridization assays 264
Bacteriophage-based methods for detection of bacteria 264
Biosensors for detection of microorganisms 265
Ibis T5000™ Biosensor System 265
DNA enzyme immunoassay 265
DNA biochip/microarray in diagnosis of infections 265
DNA-based typing methods 266
Restriction fragment length polymorphism analysis 266
Ribotyping 267
Random amplified polymorphic DNA 267
Combinatorial DNA melting assay 267
Electrochemical detection of pathogens 267
FISH for detection of infections 268
Helicase-dependent isothermal amplification for rapid detection of pathogens 268
High resolution melt analysis for diagnosis of infections 268
Ligase chain reaction 268
Mass spectrometry for microbial identification 269
Metagenomic pyrosequencing 269
Multiplex PCR for detection of infections 270
Dual priming oligonucleotide for multiplex PCR 271
LightCycler® SeptiFast Test 271
Multiplex amplified nominal tandem repeat analysis 272
VYOO® Sepsis Test 272
NASBA for detection of microorganisms 272
Nucleic acid probes 272
Neutrophil CD11b expression as a diagnostic marker 273
Optical Mapping 273
PNA-FISH for diagnosis of infections 273
QuantiFERON® technology for pre-molecular diagnosis of infections 274
Quantitative reverse-transcription PCR for bacterial diagnostics 274
Rupture event scanning 274
Real-time single-molecule imaging of virus particles 275
Single-strand conformational polymorphism 275
SmartGene platform for identifying pathogens based on genetic sequences 275
Tessera array technology 275
Unyvero Solution 276
Applications, advantages and limitations of molecular diagnostics 276
Molecular diagnostics versus other microbial detection technologies 276
Advantages of nucleic acid-based diagnostics in infections 276
Drawbacks of nucleic acid-based diagnostics in infections 277
Nanotechnology for detection of infectious agents 277
Bacterial and fungal infections 278
Mycobacterium tuberculosis 279
Conventional diagnosis of tuberculosis 280
Microscopic Observation Drug Susceptible Assay for tuberculosis 280
Molecular diagnostics for tuberculosis 280
Combined tuberculin testing and ELISpotPLUS assay 282
Biomarkers for tuberculosis 282
Diagnosis of drug-resistant M. tuberculosis infection 283
Xpert MTB/RIF automated molecular test for MTB 283
Diagnosis of other mycobacteria 284
Chlamydial infections 284
Neisseria gonorrhoeae 286
Bacteria associated with bacterial vaginosis 286
Streptococcal infections 286
Group B Streptococci 286
Streptococcus pyogenes and Streptococcus dysgalactiae 287
Pseudomonas aeruginosa 287
Helicobacter pylori 288
Lyme disease 288
Mycoplasmas 289
Fungal infections 289
Aspergillus 290
Candida species 290
Viral infections 291
HIV/AIDS 291
Diagnosis of HIV 292
Detection of HIV provirus 293
Global Surveillance of HIV-1 genetic variations 293
Genotyping for drug-resistance in HIV 293
Neonatal screening of infants of HIV-positive mothers 294
Phenotyping as predictor of drug susceptibility/resistance in HIV 294
Point-of-care testing for HIV 295
Resolution of indeterminate Western blot 296
Screening of cadaveric tissue donors 296
Tests used for quantification of HIV 296
Conclusions about HIV diagnostics 297
Hepatitis viruses 297
Hepatitis A virus 298
Hepatitis B virus 298
Hepatitis C virus 299
Detection and quantification of HCV RNA 299
Quantification of HCV RNA levels as a guide to antiviral therapy 300
Electrochemical DNA chip for diagnosis of HCV 300
HCV Genotyping as a guide to therapy 300
Enteroviruses 301
Adenoviruses 302
Rhinoviruses 302
Herpes viruses 302
Herpes simplex virus 302
Genital and neonatal herpes simplex 303
Human cytomegalovirus infections 303
Epstein-Barr virus 304
Human papilloma virus 304
Molecular diagnostics for HPV 304
Detection of encephalitis viruses 305
West Nile and St. Louis encephalitis 305
Venezuelan equine encephalitis virus 306
Detection of noroviruses 306
Protozoal infections 306
Amebiasis 306
Cryptosporidium parvum 307
Leishmaniasis 307
Malaria 307
Neurocysticercosis 308
Pneumocystis carinii 308
Toxoplasmosis 308
Infections of various systems 309
CNS infections 309
Molecular diagnosis in bacterial meningitis 309
Molecular diagnosis in herpes simplex encephalitis 309
Diagnosis of transmissible spongiform encephalopathies 310
Molecular diagnosis of respiratory viruses 311
SARS-associated coronavirus 311
Influenza viruses 312
Avian influenza 314
H1N1 influenza 318
Gastrointestinal infections 320
Periodontal infections 321
Diagnosis of urinary infections by a biosensor 322
Role of molecular diagnostics in septicemia 322
Limitations and needs of diagnostics for infections 323
Differentiation between live and antibiotic-killed bacteria 324
Cell-based methods for identifying pathogenic microorganisms 324
Cell-based virus assays 324
Cell-based detection of host response to infection 324
Role of molecular diagnostics in hospital acquired infections 325
Detection of hospital-acquired bacterial infections 325
Detection of methicillin-resistant S. aureus 325
Detection of vancomycin-resistant enterococci 326
Detection of hospital-acquired C. difficile 326
Bacterial genome sequencing in antimicrobial resistance 327
Detection of hospital-acquired viral infections 327
Molecular diagnosis of BK virus 327
Diagnosis of hospital-acquired rotavirus gastroenteritis 328
Molecular diagnostics and the microbiome 328
Human Microbiome Project 328
Application of metagenomics to study of the microbiome 329
MicroBiome Analysis Center 329
Concluding remarks and future prospects of diagnosis of infections 330
Rapid point-of-care diagnosis of infection 330
Diagnosis of viruses using protein fingerprinting 333
QIAplex PCR multiplex technology 333
Companies involved in molecular diagnosis of infectious diseases 333
7. Molecular Diagnosis of Cancer 337
Introduction 337
Cancer genomics 337
Cancer genes 338
Oncogenes 338
Tumor Suppressor Genes 338
p53 339
p16 340
CNVs in cancer 340
Allele-specific copy number analysis of tumors 341
Viruses and cancer 341
Detecting viral agents in cancer 342
Conventional cancer diagnosis 343
Molecular techniques for cancer diagnosis 343
Genome analysis at the molecular level 345
Mutation detection at molecular level 345
Expression profiling of tumor cells sorted by flow cytometry 346
MicroRNA expression profiling for cancer diagnostics 346
Biomarkers in cancer 346
Circulating nucleosomes in serum of cancer patients 347
Detection of DNA methylation 347
eTag assay system for cancer biomarkers 349
HAAH as a biomarker for cancer 350
LigAmp for detection of gene mutations in cancer 350
Mitochondrial DNA as a cancer biomarker 350
Oncoproteins as biomarkers for cancer 351
Sequencing-based approaches for detection of cancer biomarkers 351
Molecular fingerprinting of cancer 352
Fluorescent in situ hybridization 352
Genetic analysis of cancer 353
Comparative genomic hybridization in cancer diagnostics 353
Loss of heterozygosity 353
Digital karyotyping 353
Gene expression profiles predict chromosomal instability in tumors 354
PCR Techniques 354
Realtime quantitative PCR for diagnosis of cancer 355
Cold-PCR 355
Antibody-based diagnosis of cancer 355
Monoclonal antibodies for diagnosis of cancer 355
Recombinant antibodies as a novel approach to cancer diagnosis 356
Combined immunological and nucleic acid tests 356
Combination of MAbs and RT-PCR 356
Immunobead RT-PCR 356
Assays for determining susceptibility to cancer 357
Gene expression profiling in cancer 357
Microarrays for gene expression profiling in cancer 358
Serial analysis of gene expression (SAGE) 358
DNA tags for finding genes expressed in cancer 358
Suppression subtractive hybridization 359
Measurement of telomerase activity 359
Detection of circulating tumor cells in blood 360
Biochips/microfluidics for detection of CTCs 360
CellSearch 361
CellTracks® AutoPrep® System 361
CTCscope system for detection of CTCs 361
CTChip™ 361
Fiber-optic array scanning technology 361
Lab-on-chip for the isolation and detection of CTCs 362
MagSweeper 362
Future prospects of detection of cancer cells in blood 362
Epithelial aggregate separation and isolation 363
Proteomic technologies for the molecular diagnosis of cancer 363
Proteomic technologies for tumor biomarkers 363
Affibodies as contrast agents for imaging in cancer 364
Aptamer-based technology for protein signatures of cancer cells 364
Aptamer probes for in vivo diagnosis of cancer 364
Aptamers for combined diagnosis and therapeutics of cancer 365
Automated image analysis of nuclear protein distribution 365
Laser capture microdissection in oncology 366
Layered expression scanning 366
Membrane-type serine protease-1 366
Survivin and molecular diagnosis of cancer 367
Biochip/microarrays for cancer diagnosis 367
Role of DNA microarrays in gene expression profiling 368
Biochip detection of FHIT gene 368
Nanobiotechnology for e
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